ArticlePlant & cell physiology2011
ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.
Article in Plant & cell physiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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73 citing papers in PubMed.
- An Introduction to Network Analysis in Plant Biology.Plant direct · 2025Article
- NetREx: Network-based Rice Expression Analysis Server for abiotic stress conditions.Database : the journal of biological databases and curation · 2022Article
- Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production.Breeding science · 2021Article
- A Thylakoid Membrane Protein Functions Synergistically with GUN5 in Chlorophyll Biosynthesis.Plant communications · 2020Article
- METACLUSTER-an R package for context-specific expression analysis of metabolic gene clusters.Bioinformatics (Oxford, England) · 2019Article
- Long-Day Photoperiod Enhances Jasmonic Acid-Related Plant Defense.Plant physiology · 2018Article
- Co-expression network analysis and cis-regulatory element enrichment determine putative functions and regulatory mechanisms of grapevine ATL E3 ubiquitin ligases.Scientific reports · 2018Article
- ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index.Plant & cell physiology · 2018Article
- Gene Discovery of Characteristic Metabolic Pathways in the Tea Plant (Frontiers in plant science · 2018Review
- Extracellular ATP Acts on Jasmonate Signaling to Reinforce Plant Defense.Plant physiology · 2018Article
- Genome-wide analysis of cis-regulatory element structure and discovery of motif-driven gene co-expression networks in grapevine.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Constructing Integrated Networks for Identifying New Secondary Metabolic Pathway Regulators in Grapevine: Recent Applications and Future Opportunities.Frontiers in plant science · 2017Article
- FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants.Plant physiology · 2016Article
- Identification and Network-Enabled Characterization of Auxin Response Factor Genes inFrontiers in plant science · 2016Article
- ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression.Plant & cell physiology · 2016Article
- Transcriptome analysis of hormone-induced gene expression in Brachypodium distachyon.Scientific reports · 2015Article
- Volatile Glycosylation in Tea Plants: Sequential Glycosylations for the Biosynthesis of Aroma β-Primeverosides Are Catalyzed by Two Camellia sinensis Glycosyltransferases.Plant physiology · 2015Article
- The jasmonate-responsive GTR1 transporter is required for gibberellin-mediated stamen development in Arabidopsis.Nature communications · 2015Article
- Antagonistic roles for KNOX1 and KNOX2 genes in patterning the land plant body plan following an ancient gene duplication.PLoS genetics · 2015Article
- GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response.Nucleic acids research · 2015Article
13 more citing papers are in PubMed but not listed here.
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Abstract
ATTED-II (http://atted.jp) is a gene coexpression database for a wide variety of experimental designs, such as prioritizations of genes for functional identification and analyses of the regulatory relationships among genes. Here, we report updates of ATTED-II focusing on two new features: condition-specific coexpression and homologous coexpression with rice. To analyze a broad range of biological phenomena, it is important to collect data under many diverse experimental conditions, but the meaning of coexpression can become ambiguous under these conditions. One approach to overcome this difficulty is to calculate the coexpression for each set of conditions with a clear biological meaning. With this viewpoint, we prepared five sets of experimental conditions (tissue, abiotic stress, biotic stress, hormones and light conditions), and users can evaluate the coexpression by employing comparative gene lists and switchable gene networks. We also developed an interactive visualization system, using the Cytoscape web system, to improve the network representation. As the second update, rice coexpression is now available. The previous version of ATTED-II was specifically developed for Arabidopsis, and thus coexpression analyses for other useful plants have been difficult. To solve this problem, we extended ATTED-II by including comparison tables between Arabidopsis and rice. This representation will make it possible to analyze the conservation of coexpression among flowering plants. With the ability to investigate condition-specific coexpression and species conservation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in a broad array of plant species.
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